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This commit is contained in:
Jeremy Goecks
@@ -32,47 +32,12 @@ class Genome( object ):
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self.key = key
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self.len_file = len_file
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self.twobit_file = twobit_file
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class Genomes( object ):
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"""
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Provides information about available genome data and methods for manipulating that data.
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"""
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def __init__( self, app ):
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# Create list of known genomes from len files.
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self.genomes = {}
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len_files = glob.glob( os.path.join( app.config.len_file_path, "*.len" ) )
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for f in len_files:
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key = os.path.split( f )[1].split( ".len" )[0]
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self.genomes[ key ] = Genome( key, len_file=f )
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# Add genome data (twobit files) to genomes.
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for line in open( os.path.join( app.config.tool_data_path, "twobit.loc" ) ):
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if line.startswith("#"): continue
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val = line.split()
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if len( val ) == 2:
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key, path = val
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if key in self.genomes:
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self.genomes[ key ].twobit_file = path
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def get_dbkeys_with_chrom_info( self, trans ):
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""" Returns all valid dbkeys that have chromosome information. """
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# All user keys have a len file.
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user_keys = {}
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user = trans.get_user()
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if 'dbkeys' in user.preferences:
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user_keys = from_json_string( user.preferences['dbkeys'] )
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dbkeys = [ (v, k) for k, v in trans.db_builds if ( ( k in self.genomes and self.genomes[ k ].len_file ) or k in user_keys ) ]
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return dbkeys
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def chroms( self, trans, dbkey=None, num=None, chrom=None, low=None ):
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def to_dict( self, num=None, chrom=None, low=None ):
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"""
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Returns a naturally sorted list of chroms/contigs for a given dbkey.
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Use either chrom or low to specify the starting chrom in the return list.
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Returns representation of self as a dictionary.
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"""
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def check_int(s):
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if s.isdigit():
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return int(s)
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@@ -97,47 +62,13 @@ class Genomes( object ):
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else:
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low = 0
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# If there is no dbkey owner, default to current user.
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dbkey_owner, dbkey = decode_dbkey( dbkey )
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if dbkey_owner:
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dbkey_user = trans.sa_session.query( trans.app.model.User ).filter_by( username=dbkey_owner ).first()
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else:
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dbkey_user = trans.user
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#
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# Get len file.
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#
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# Look first in user's custom builds.
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len_file = None
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len_ds = None
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user_keys = {}
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if dbkey_user and 'dbkeys' in dbkey_user.preferences:
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user_keys = from_json_string( dbkey_user.preferences['dbkeys'] )
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if dbkey in user_keys:
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dbkey_attributes = user_keys[ dbkey ]
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if 'fasta' in dbkey_attributes:
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build_fasta = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dbkey_attributes[ 'fasta' ] )
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len_file = build_fasta.get_converted_dataset( trans, 'len' ).file_name
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# Backwards compatibility: look for len file directly.
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elif 'len' in dbkey_attributes:
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len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[ dbkey ][ 'len' ] ).file_name
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# Look in system builds.
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if not len_file:
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len_ds = trans.db_dataset_for( dbkey )
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if not len_ds:
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len_file = self.genomes[ dbkey ].len_file
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else:
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len_file = len_ds.file_name
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#
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# Get chroms data:
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# (a) chrom name, len;
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# (b) whether there are previous, next chroms;
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# (c) index of start chrom.
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#
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len_file_enumerate = enumerate( open( len_file ) )
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len_file_enumerate = enumerate( open( self.len_file ) )
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chroms = {}
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prev_chroms = False
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start_index = 0
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@@ -169,11 +100,6 @@ class Genomes( object ):
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start_index = low
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# Read chrom data from len file.
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# TODO: this may be too slow for very large numbers of chroms/contigs,
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# but try it out for now.
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if not os.path.exists( len_file ):
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return None
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for line_num, line in len_file_enumerate:
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if line_num < low:
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continue
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@@ -197,9 +123,99 @@ class Genomes( object ):
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to_sort = [{ 'chrom': chrom, 'len': length } for chrom, length in chroms.iteritems()]
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to_sort.sort(lambda a,b: cmp( split_by_number(a['chrom']), split_by_number(b['chrom']) ))
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return { 'reference': self.has_reference_data( trans, dbkey, dbkey_user ), 'chrom_info': to_sort,
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'prev_chroms' : prev_chroms, 'next_chroms' : next_chroms, 'start_index' : start_index }
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return {
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'id': self.key,
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'reference': self.twobit_file is not None,
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'chrom_info': to_sort,
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'prev_chroms' : prev_chroms,
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'next_chroms' : next_chroms,
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'start_index' : start_index
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}
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class Genomes( object ):
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"""
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Provides information about available genome data and methods for manipulating that data.
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"""
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def __init__( self, app ):
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# Create list of known genomes from len files.
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self.genomes = {}
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len_files = glob.glob( os.path.join( app.config.len_file_path, "*.len" ) )
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for f in len_files:
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key = os.path.split( f )[1].split( ".len" )[0]
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self.genomes[ key ] = Genome( key, len_file=f )
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# Add genome data (twobit files) to genomes.
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for line in open( os.path.join( app.config.tool_data_path, "twobit.loc" ) ):
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if line.startswith("#"): continue
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val = line.split()
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if len( val ) == 2:
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key, path = val
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if key in self.genomes:
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self.genomes[ key ].twobit_file = path
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def get_build( self, dbkey ):
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""" Returns build for the given key. """
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rval = None
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if dbkey in self.genomes:
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rval = self.genomes[ dbkey ]
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return rval
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def get_dbkeys_with_chrom_info( self, trans ):
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""" Returns all valid dbkeys that have chromosome information. """
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# All user keys have a len file.
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user_keys = {}
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user = trans.get_user()
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if 'dbkeys' in user.preferences:
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user_keys = from_json_string( user.preferences['dbkeys'] )
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dbkeys = [ (v, k) for k, v in trans.db_builds if ( ( k in self.genomes and self.genomes[ k ].len_file ) or k in user_keys ) ]
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return dbkeys
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def chroms( self, trans, dbkey=None, num=None, chrom=None, low=None ):
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"""
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Returns a naturally sorted list of chroms/contigs for a given dbkey.
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Use either chrom or low to specify the starting chrom in the return list.
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"""
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# If there is no dbkey owner, default to current user.
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dbkey_owner, dbkey = decode_dbkey( dbkey )
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if dbkey_owner:
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dbkey_user = trans.sa_session.query( trans.app.model.User ).filter_by( username=dbkey_owner ).first()
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else:
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dbkey_user = trans.user
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#
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# Get/create genome object.
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#
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genome = None
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# Look first in user's custom builds.
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if dbkey_user and 'dbkeys' in dbkey_user.preferences:
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user_keys = from_json_string( dbkey_user.preferences['dbkeys'] )
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if dbkey in user_keys:
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dbkey_attributes = user_keys[ dbkey ]
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if 'fasta' in dbkey_attributes:
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build_fasta = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dbkey_attributes[ 'fasta' ] )
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len_file = build_fasta.get_converted_dataset( trans, 'len' ).file_name
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# Backwards compatibility: look for len file directly.
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elif 'len' in dbkey_attributes:
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len_file = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( user_keys[ dbkey ][ 'len' ] ).file_name
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if len_file:
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genome = Genome( dbkey, len_file=len_file )
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# Look in system builds.
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if not genome:
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len_ds = trans.db_dataset_for( dbkey )
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if not len_ds:
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genome = self.genomes[ dbkey ]
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else:
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gneome = Genome( dbkey, len_file=len_ds.file_name )
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return genome.to_dict( num=num, chrom=chrom, low=low )
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def has_reference_data( self, trans, dbkey, dbkey_owner=None ):
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"""
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Returns true if there is reference data for the specified dbkey. If dbkey is custom,
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